ProfileMD script builds energy profile as function of the dihedral angle between the atoms of the molecule. It executes energy minimization and constrained dynamics for the range of angle values and writes down resulting average energies.

initially written by
Tatiana V. Galochkina
email: tat.galochkina@gmail.com

Université Sorbonne Paris Cité, Université Paris Diderot, Inserm, INTS
Unité Biologie Intégrée du Globule Rouge UMR S1134, DSIMB, Laboratoire d’Excellence GR-Ex

To run this script you should have to fit the following requirements:

1. File start.gro should exist

   This is a regular structure file of your molecule.

2. File dih.ndx should exist

   This is an index file with exactly one group containing exactly four atoms. These four atoms define the angle of rotation. All other lines of the file are ignored.

3. File temp.top should exist

   Your topology file should have "#define mydih" definition of improper dihedral at 10th line. In [dihedrals] section you should set to "mydih" your angle of interest (the same as prescribed in your dih.ndx file). NOTE that all other diherdrals around the same valence bond must be turned off. Please take a look on lines 183-188 of the example file.

4. GROMACS version > 5.*

   Our script is designed for running all the commands through gmx application wrapper.

5. You should have protocols of energy minimization and constrained dynamics.

   You can use em.mdp and run.mdp provided in our example. NOTE that you should not use PME to calculate electrostatic interactions for small system in a big box. It would lead the useless increase of the CPU time.

Once all the listed files are prepared you can run ProfileMD. To check if the script gives a correct result, take a look on the output _*.pdb file. Please be careful while preparing your topology and selecting terms from the energy output. By default the script collects first 14 terms from EDR files. If you include some special energy groups you may be interested in increasing this number. In this case please address GetEnergy function.

All intermediate calculations are stored in the scratch folder. To repeat the scan procedure you should remove scratch folder or change its name.

Load force field from this repository, save it to charmm36.ff folder here and then run ProfileMD.py from the current directory.